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<div class="h1">
Contents
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<div class="h2">
<name="algorithm">
Algorithm
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<div class="txt">
<table>
<tr><td valign="top"><a href="abortoptim.html">abortoptim</a></td><td>Determines whether all parameters have sufficiently converged</td></tr>
<tr><td valign="top"><a href="allcomb.html">allcomb</a></td><td>Computes all combinations of the elements of the input arguments. Implemented by Jos van der Geest. See <a href="matlab:web('http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=10064&objectType=FILE','-browser')">www.mathworks.com</a>. </td></tr>
<tr><td valign="top"><a href="calccbwb.html">calccbwb</a></td><td>Calculates two shape parameters 'c(&#946;)' and '&#969(&#946;)' for exponential power distributions</td></tr>
<tr><td valign="top"><a href="covRandomDraw.html">covRandomDraw</a></td><td>Generates the initial samples based on the covariance matrix.</td></tr>
<tr><td valign="top"><a href="calcobjscore.html">calcobjscore</a></td><td>Runs the model and evaluates the objective function</td></tr>
<tr><td valign="top"><a href="continueDream.html">continueDream</a></td><td>Determine whether the optimization algorithm should still go on</td></tr>
<tr><td valign="top"><a href="evolve.html">evolve</a></td><td>Applies a Metropolis annealing method to evolve the sequences</td></tr>
<tr><td valign="top"><a href="foldBounds.html">foldBounds</a></td><td>Generates new points by folding the bounds that are excedeed.</td></tr>
<tr><td valign="top"><a href="gelmanRubin.html">gelmanRubin</a></td><td>Calculates the Gelman-Rubin potential scale reduction statistic </td></tr>
<tr><td valign="top"><a href="generateOffspring.html">generateOffspring</a></td><td>Proposes new offspring</td></tr>
<tr><td valign="top"><a href="generateCrossoverValues.html">generateCrossoverValues</a></td><td>Associates to each point in all the generations and sequences a  crossover probability</td></tr>
<tr><td valign="top"><a href="getDiffEvolStrategy.html">getDiffEvolStrategy</a></td><td>Associates to each sequence a differential evolution strategy</td></tr>
<tr><td valign="top"><a href="toSequences.html">toSequences</a></td><td>Partitions evenly the evaluated points into sequences</td></tr>
<tr><td valign="top"><a href="dream.html">dream</a></td><td>Main program of the optimization algorithm</td></tr>
<!--<tr><td valign="top"><a href="seedsample.html">seedsample</a></td><td>Initializes the pseudorandom generator</td></tr>-->
<tr><td valign="top"><a href="reflectBounds.html">reflectBounds</a></td><td>Generates new points by reflecting against the bound that was exceeded.</td></tr>
<tr><td valign="top"><a href="setToBounds.html">setToBounds</a></td><td>Generates new points by replacing the old ones with the bound that was exceeded.</td></tr>
<tr><td valign="top"><a href="stratranddraw.html">stratranddraw</a></td><td>Stratified random sampling</td></tr>
<tr><td valign="top"><a href="unifranddraw.html">unifranddraw</a></td><td>Uniform random sampling</td></tr>
<tr><td valign="top"><a href="updateDelta.html">updateDelta</a></td><td>Calculates the total normalized Euclidean distance between the old and the new points.</td></tr>
<tr><td valign="top"><a href="updatePCrossover.html">updatePCrossover</a></td><td>Updates the probabilities of the various crossover values</td></tr>
<tr><td valign="top"><a href="updateSequences.html">updateSequences</a></td><td>Updates the sequences array by adding the last accepted points in each of the sequences</td></tr>

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<div class="h2">
Visualization
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<tr><td valign="top"><a href="marghist.html">marghist</a></td><td>Visualizes the multidimensional density distribution using marginal 1D histograms</td></tr>
<tr><td valign="top"><a href="matrixofcontourf.html">matrixofcontourf</a></td><td>Visualizes the multidimensional density distribution using a matrix of marginal 2D filled contour plots</td></tr>
<tr><td valign="top"><a href="matrixofimagesc.html">matrixofimagesc</a></td><td>Visualizes the multidimensional density distribution using a matrix of marginal 2D histograms</td></tr>
<tr><td valign="top"><a href="matrixofscatter.html">matrixofscatter</a></td><td>Visualizes the multidimensional density distribution using a matrix of marginal 2D scatter plots</td></tr>
<tr><td valign="top"><a href="plotconv.html">plotconv</a></td><td>Visualizes how parameter values converge with iteration</td></tr>
<tr><td valign="top"><a href="plotgelmanrubin.html">plotgelmanrubin</a></td><td>Visualizes how the Gelman-Rubin scale reduction criterion varies with each generation</td></tr>
<tr><td valign="top"><a href="plotobj.html">plotobj</a></td><td>Visualizes how the objective score changes with iteration</td></tr>
<tr><td valign="top"><a href="plotseq.html">plotseq</a></td><td>Visualizes how sequences are shuffled collections of parameters</td></tr>
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<div class="h2">
Tools
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<div class="txt">
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<tr><td valign="top"><a href="bayesprobint.html">bayesprobint</a></td><td>Calculate bayesian probability intervals</td></tr>
<tr><td valign="top"><a href="buildconstantsmap.html">buildconstantsmap</a></td><td>Build a map of which variables should be imported as model constants</td></tr>
<tr><td valign="top"><a href="buildparametermap.html">buildparametermap</a></td><td>Build a map of which variables should be imported as model parameters</td></tr>
<tr><td valign="top"><a href="effnasu.html">effnasu</a></td><td>Calculate Nash-Sutcliffe efficiency</td></tr>
<tr><td valign="top"><a href="ggobiexport.html">ggobiexport</a></td><td>Export data to a file format that can be read by the multi-dimensional visualization program <a href="matlab: web('http://www.ggobi.org','-browser')">ggobi</a></td></tr>
<tr><td valign="top"><a href="importconstants.html">importconstants</a></td><td>Import the variables that have been listed as model constants</td></tr>
<tr><td valign="top"><a href="importmeasurements.html">importmeasurements</a></td><td>Import the variables that have been listed as measurements</td></tr>
<tr><td valign="top"><a href="importparameters.html">importparameters</a></td><td>Import the variables that have been listed as model parameters</td></tr>
</table>

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